Abstract
Recent advances in DNA sequencing and mass spectrometry technologies have allowed us to collect more data on microbiome and metabolome to assess the influence of the gut microbiota on human health at a whole-systems level. Major advances in metagenomics and metabolomics technologies have shown that the gut microbiota contributes to host overall health status to a large extent. As such, the gut microbiota is often likened to a measurable and functional organ consisting of prokaryotic cells, which creates the unique gut ecosystem together with the host eukaryotic cells. In this review, we discuss in detail the relationship between gut microbiota and its metabolites like choline, bile acids, phenols, and short-chain fatty acids in the host health and etiopathogenesis of various pathological states such as multiple sclerosis, autism, obesity, diabetes, and chronic kidney disease. By integrating metagenomic and metabolomic information on a systems biology-wide approach, we would be better able to understand this interplay between gut microbiome and host metabolism. Integration of the microbiome, metatranscriptome, and metabolome information will pave the way toward an improved holistic understanding of the complex mammalian superorganism. Through the modeling of metabolic interactions between lifestyle, diet, and microbiota, integrated omics-based understanding of the gut ecosystem is the new avenue, providing exciting novel therapeutic approaches for optimal host health.
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Tringe S, Hugenholtz P (2008) A renaissance for the pionnering 16S rRNA gene. Curr Opin Microbiol 11:442–446
Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S (2012) Host-gut microbiota metabolic interactions. Science 336:1262–1267
Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031
Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC, Hu C, Wong FS, Szot GL, Bluestone JA, Gordon JI, Chervonsky AV (2008) Innate immunity and intestinal microbiota in the development of type 1 diabetes. Nature 455:1109–1113
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Meta HITC, Bork P, Ehrlich SD, Wang J (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65
Kirjavainen P, Arvola T, Salminen S, Isolauri E (2002) Aberrant composition of gut microbiota of allergic infants: a target of bifidobacterial therapy at weaning? Gut 51:51–55
Berer K, Mues M, Koutrolos M, Rasbi ZA, Boziki M, Johner C, Wekerle H, Krishnamoorthy G (2011) Commensal microbiota and myelin autoantigen cooperate to trigger autoimmune demyelination. Nature 479:538–541
Finegold SM (2008) Therapy and epidemiology of autism–clostridial spores as key elements. Med Hypotheses 70:508–511
Wang F, Zhang P, Jiang H, Cheng S (2012) Gut bacterial translocation contributes to microinflammation in experimental uremia. Dig Dis Sci 57:2856–2862
Marchesi J, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, Wilson I, Wang Y (2007) Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 6:546–551
Scanlan PD, Shanahan F, Clune Y, Collins JK, O'Sullivan GC, O'Riordan M, Holmes E, Wang Y, Marchesi JR (2008) Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol 10:789–798
Clayton TA, Lindon JC, Cloarec O, Antti H, Charuel C, Hanton G, Provost JP, Le Net JL, Baker D, Walley RJ, Everett JR, Nicholson JK (2006) Pharmaco-metabonomic phenotyping and personalized drug treatment. Nature 440:1073–1077
Hooper LV (2001) Commensal host-bacterial relationships in the gut. Science 292:1115–1118
Macpherson AJ (2000) A primitive T cell-independent mechanism of intestinal mucosal IgA responses to commensal bacteria. Science 288:2222–2226
Kinross J, Alkhamesi N, Barton R, Silk D, Yap I, Darzi A, Holmes E, Nicholson J (2011) Global metabolic phenotyping in an experimental laparotomy model of surgical trauma. J Proteome Res 10:277–287
Bianconi E, Piovesan A, Facchin F, Beraudi A, Casadei R, Frabetti F, Vitale L, Pelleri MC, Tassani S, Piva F, Perez-Amodio S, Strippoli P, Canaider S (2013) An estimation of the number of cells in the human body. Ann Hum Biol 40:463–471
Fukuda S, Ohno H (2014) Gut microbiome and metabolic diseases. Semin Immunopathol 36:103–114
Xu J, Mahowald M, Ley R, Lozupone C, Hamady M, Martens E, Henrissat B, Coutinho P, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton R, Fulton L, Clifton S, Wilson R, Knight R, Gordon J (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5:1574–1586
Dettmer K, Aronov P, Hammock B (2007) Mass spectrometry based metabolomics. Mass Spectrom Rev 26:51–78
Wenk MR (2005) The emerging field of lipidomics. Nat Rev Drug Discov 4:594–610
Buescher J, Moco S, Sauer U, Zamboni N (2010) Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites. Anal Chem 82:4403–4412
Moco S, Bino RJ, Vorst O, Verhoeven HA, de Groot J, van Beek TA, Vervoort J, de Vos CH (2006) A liquid chromatography-mass spectrometry-based metabolome database for tomato. Plant Physiol 141:1205–1218
Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA, Peters EC, Siuzdak G (2009) Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci U S A 106:3698–3703
Martin FP, Wang Y, Sprenger N, Yap IK, Lundstedt T, Lek P, Rezzi S, Ramadan Z, van Bladeren P, Fay LB, Kochhar S, Lindon JC, Holmes E, Nicholson JK (2008) Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model. Mol Syst Biol 4:157
Nicholson J, Wilson I (2003) Understanding 'global' systems biology metabonomics and the continuum of metabolism. Nat Rev Drug Discov 2:668–676
Vance D (2008) Role of phosphatidylcholine biosynthesis in the regulation of lipoprotein homeostasis. Curr Opin Lipidol 19:229–234
Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ, Strowig T, Thaiss CA, Kau AL, Eisenbarth SC, Jurczak MJ, Camporez JP, Shulman GI, Gordon JI, Hoffman HM, Flavell RA (2012) Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482:179–185
Spencer MD, Hamp TJ, Reid RW, Fischer LM, Zeisel SH, Fodor AA (2011) Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency. Gastroenterology 140:976–986
Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, Dugar B, Feldstein AE, Britt EB, Fu X, Chung YM, Wu Y, Schauer P, Smith JD, Allayee H, Tang WH, DiDonato JA, Lusis AJ, Hazen SL (2011) Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472:57–63
Dumas ME, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside J, Tatoud R, Blanc V, Lindon JC, Mitchell SC, Holmes E, McCarthy MI, Scott J, Gauguier D, Nicholson JK (2006) Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci U S A 103:12511–12516
Prentiss P, Rosen H, Brown N, Horowitz R, Malm O, Levenson S (1961) The metabolism of choline by the germfree rat. Arch Biochem Biophys 94:424–429
Tang WH, Wang Z, Levison BS, Koeth RA, Britt EB, Fu X, Wu Y, Hazen SL (2013) Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med 368:1575–1584
Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, Smith JD, DiDonato JA, Chen J, Li H, Wu GD, Lewis JD, Warrier M, Brown JM, Krauss RM, Tang WH, Bushman FD, Lusis AJ, Hazen SL (2013) Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med 19:576–585
Swann JR, Want EJ, Geier FM, Spagou K, Wilson ID, Sidaway JE, Nicholson JK, Holmes E (2011) Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. Proc Natl Acad Sci U S A 108(Suppl 1):4523–4530
Ridlon JM, Kang DJ, Hylemon PB (2006) Bile salt biotransformations by human intestinal bacteria. J Lipid Res 47:241–259
Watanabe M, Houten SM, Mataki C, Christoffolete MA, Kim BW, Sato H, Messaddeq N, Harney JW, Ezaki O, Kodama T, Schoonjans K, Bianco AC, Auwerx J (2006) Bile acids induce energy expenditure by promoting intracellular thyroid hormone activation. Nature 439:484–489
Friedman SL (2008) Hepatic stellate cells: protean, multifunctional, and enigmatic cells of the liver. Physiol Rev 88:125–172
Orjalo AV, Bhaumik D, Gengler BK, Scott GK, Campisi J (2009) Cell surface-bound IL-1alpha is an upstream regulator of the senescence-associated IL-6/IL-8 cytokine network. Proc Natl Acad Sci U S A 106:17031–17036
Coulouarn C, Corlu A, Glaise D, Guenon I, Thorgeirsson SS, Clement B (2012) Hepatocyte-stellate cell cross-talk in the liver engenders a permissive inflammatory microenvironment that drives progression in hepatocellular carcinoma. Cancer Res 72:2533–2542
Yoshimoto S, Loo TM, Atarashi K, Kanda H, Sato S, Oyadomari S, Iwakura Y, Oshima K, Morita H, Hattori M, Honda K, Ishikawa Y, Hara E, Ohtani N (2013) Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome. Nature 499:97–101
Wostmann B (1973) Intestinal bile acids and cholesterol absorption in the germfree rat. J Nutr 103:982–990
Prawitt J, Abdelkarim M, Stroeve J, Popescu I, Duez H, Velagapudi V, Dumont J, Bouchaert E, van Dijk T, Lucas A, Dorchies E, Daoudi M, Lestavel S, Gonzalez F, Oresic M, Cariou B, Kuipers F, Caron S, Staels B (2011) Farnesoid X receptor deficiency improves glucose homeostasis in mouse models of obesity. Diabetes 60:1861–1871
Thomas C, Gioiello A, Noriega L, Strehle A, Oury J, Rizzo G, Macchiarulo A, Yamamoto H, Mataki C, Pruzanski M, Pellicciari R, Auwerx J, Schoonjans K (2009) TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab 10:167–177
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559–563
Jones BV, Begley M, Hill C, Gahan CG, Marchesi JR (2008) Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A 105:13580–13585
Bone E, Tamm A, Hill M (1976) The production of urinary phenols by gut bacteria and their possible role in the causation of large bowel cancer. Am J Clin Nutr 29:1448–1457
Ott SJ (2004) Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53:685–693
Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 102:11070–11075
Samuel BS, Shaito A, Motoike T, Rey FE, Backhed F, Manchester JK, Hammer RE, Williams SC, Crowley J, Yanagisawa M, Gordon JI (2008) Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proc Natl Acad Sci U S A 105:16767–16772
Maslowski KM, Vieira AT, Ng A, Kranich J, Sierro F, Yu D, Schilter HC, Rolph MS, Mackay F, Artis D, Xavier RJ, Teixeira MM, Mackay CR (2009) Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature 461:1282–1286
Sina C, Gavrilova O, Forster M, Till A, Derer S, Hildebrand F, Raabe B, Chalaris A, Scheller J, Rehmann A, Franke A, Ott S, Hasler R, Nikolaus S, Folsch UR, Rose-John S, Jiang HP, Li J, Schreiber S, Rosenstiel P (2009) G protein-coupled receptor 43 is essential for neutrophil recruitment during intestinal inflammation. J Immunol 183:7514–7522
Kimura I, Ozawa K, Inoue D, Imamura T, Kimura K, Maeda T, Terasawa K, Kashihara D, Hirano K, Tani T, Takahashi T, Miyauchi S, Shioi G, Inoue H, Tsujimoto G (2013) The gut microbiota suppresses insulin-mediated fat accumulation via the short-chain fatty acid receptor GPR43. Nat Commun 4:1829
Tolhurst G, Heffron H, Lam Y, Parker H, Habib A, Diakogiannaki E, Cameron J, Grosse J, Reimann F, Gribble F (2012) Short-chain fatty acids stimulate glucagon-like peptide-1 secretion via the G-protein-coupled receptor FFAR2. Diabetes 61:364–371
Donohoe DR, Garge N, Zhang X, Sun W, O'Connell TM, Bunger MK, Bultman SJ (2011) The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab 13:517–526
Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G, Takahashi D, Nakanishi Y, Uetake C, Kato K, Kato T, Takahashi M, Fukuda NN, Murakami S, Miyauchi E, Hino S, Atarashi K, Onawa S, Fujimura Y, Lockett T, Clarke JM, Topping DL, Tomita M, Hori S, Ohara O, Morita T, Koseki H, Kikuchi J, Honda K, Hase K, Ohno H (2013) Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504:446–450
Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, Cheng G, Yamasaki S, Saito T, Ohba Y, Taniguchi T, Takeda K, Hori S, Ivanov II, Umesaki Y, Itoh K, Honda K (2011) Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331:337–341
Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, Fukuda S, Saito T, Narushima S, Hase K, Kim S, Fritz JV, Wilmes P, Ueha S, Matsushima K, Ohno H, Olle B, Sakaguchi S, Taniguchi T, Morita H, Hattori M, Honda K (2013) Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500:232–236
Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, Marsland BJ (2014) Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 20:159–166
Tremaroli V, Backhed F (2012) Functional interactions between the gut microbiota and host metabolism. Nature 489:242–249
MacFabe DF, Cain NE, Boon F, Ossenkopp KP, Cain DP (2011) Effects of the enteric bacterial metabolic product propionic acid on object-directed behavior, social behavior, cognition, and neuroinflammation in adolescent rats: relevance to autism spectrum disorder. Behav Brain Res 217:47–54
De Vadder F, Kovatcheva-Datchary P, Goncalves D, Vinera J, Zitoun C, Duchampt A, Backhed F, Mithieux G (2014) Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits. Cell 156:84–96
Singh N, Gurav A, Sivaprakasam S, Brady E, Padia R, Shi H, Thangaraju M, Prasad PD, Manicassamy S, Munn DH, Lee JR, Offermanns S, Ganapathy V (2014) Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis. Immunity 40:128–139
Fukuda S, Toh H, Hase K, Oshima K, Nakanishi Y, Yoshimura K, Tobe T, Clarke JM, Topping DL, Suzuki T, Taylor TD, Itoh K, Kikuchi J, Morita H, Hattori M, Ohno H (2011) Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469:543–547
Okada T, Fukuda S, Hase K, Nishiumi S, Izumi Y, Yoshida M, Hagiwara T, Kawashima R, Yamazaki M, Oshio T, Otsubo T, Inagaki-Ohara K, Kakimoto K, Higuchi K, Kawamura YI, Ohno H, Dohi T (2013) Microbiota-derived lactate accelerates colon epithelial cell turnover in starvation-refed mice. Nat Commun 4:1654
Hawrelak J, Myers S (2004) The causes of intestinal dysbiosis: a review. Altern Med Rev 9:180–197
Ochoa-Reparaz J, Mielcarz DW, Ditrio LE, Burroughs AR, Foureau DM, Haque-Begum S, Kasper LH (2009) Role of gut commensal microflora in the development of experimental autoimmune encephalomyelitis. J Immunol 183:6041–6050
Lee YK, Menezes JS, Umesaki Y, Mazmanian SK (2011) Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proc Natl Acad Sci U S A 108(Suppl 1):4615–4622
Buie T, Campbell DB, Fuchs GJ 3rd, Furuta GT, Levy J, Vandewater J, Whitaker AH, Atkins D, Bauman ML, Beaudet AL, Carr EG, Gershon MD, Hyman SL, Jirapinyo P, Jyonouchi H, Kooros K, Kushak R, Levitt P, Levy SE, Lewis JD, Murray KF, Natowicz MR, Sabra A, Wershil BK, Weston SC, Zeltzer L, Winter H (2010) Evaluation, diagnosis, and treatment of gastrointestinal disorders in individuals with ASDs: a consensus report. Pediatrics 125(Suppl 1):S1–S18
Coury DL, Ashwood P, Fasano A, Fuchs G, Geraghty M, Kaul A, Mawe G, Patterson P, Jones NE (2012) Gastrointestinal conditions in children with autism spectrum disorder: developing a research agenda. Pediatrics 130(Suppl 2):S160–S168
Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, Youn E, Summanen PH, Granpeesheh D, Dixon D, Liu M, Molitoris DR, Green JA 3rd (2010) Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe 16:444–453
Finegold SM, Downes J, Summanen PH (2012) Microbiology of regressive autism. Anaerobe 18:260–262
Kang DW, Park JG, Ilhan ZE, Wallstrom G, Labaer J, Adams JB, Krajmalnik-Brown R (2013) Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLoS One 8:e68322
Parracho HM, Bingham MO, Gibson GR, McCartney AL (2005) Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. J Med Microbiol 54:987–991
Williams BL, Hornig M, Buie T, Bauman ML, Cho Paik M, Wick I, Bennett A, Jabado O, Hirschberg DL, Lipkin WI (2011) Impaired carbohydrate digestion and transport and mucosal dysbiosis in the intestines of children with autism and gastrointestinal disturbances. PLoS One 6:e24585
Williams BL, Hornig M, Parekh T, Lipkin WI (2012) Application of novel PCR-based methods for detection, quantitation, and phylogenetic characterization of Sutterella species in intestinal biopsy samples from children with autism and gastrointestinal disturbances. MBio 3
Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, Patterson PH, Mazmanian SK (2013) Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 155:1451–1463
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI (2009) A core gut microbiome in obese and lean twins. Nature 457:480–484
Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, Sitaraman SV, Knight R, Ley RE, Gewirtz AT (2010) Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328:228–231
Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI (2013) Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341:1241214
Kalliomäki M, Collado M, Salminen S, Isolauri E (2008) Early differences in fecal microbiota composition in children may predict overweight. Am J Clin Nutr 87(3):534–538
Karlsson CL, Onnerfalt J, Xu J, Molin G, Ahrne S, Thorngren-Jerneck K (2012) The microbiota of the gut in preschool children with normal and excessive body weight. Obesity (Silver Spring) 20:2257–2261
Belzer C, de Vos WM (2012) Microbes inside–from diversity to function: the case of Akkermansia. ISME J 6:1449–1458
Everard A, Belzer C, Geurts L, Ouwerkerk J, Druart C, Bindels L, Guiot Y, Derrien M, Muccioli G, Delzenne N, de Vos W, Cani P (2013) Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci U S A 110:9066–9071
Everard A, Lazarevic V, Derrien M, Girard M, Muccioli G, Neyrinck A, Possemiers S, Van Holle A, François P, de Vos W, Delzenne N, Schrenzel J, Cani P (2011) Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice. Diabetes 60:2775–2786
Collado M, Isolauri E, Laitinen K, Salminen S (2008) Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am J Clin Nutr 88:894–899
Santacruz A, Collado MC, Garcia-Valdes L, Segura MT, Martin-Lagos JA, Anjos T, Marti-Romero M, Lopez RM, Florido J, Campoy C, Sanz Y (2010) Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women. Br J Nutr 104:83–92
Hansen CH, Krych L, Nielsen DS, Vogensen FK, Hansen LH, Sorensen SJ, Buschard K, Hansen AK (2012) Early life treatment with vancomycin propagates Akkermansia muciniphila and reduces diabetes incidence in the NOD mouse. Diabetologia 55:2285–2294
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, Xue W, Li J, Han L, Lu D, Wu P, Dai Y, Sun X, Li Z, Tang A, Zhong S, Li X, Chen W, Xu R, Wang M, Feng Q, Gong M, Yu J, Zhang Y, Zhang M, Hansen T, Sanchez G, Raes J, Falony G, Okuda S, Almeida M, LeChatelier E, Renault P, Pons N, Batto JM, Zhang Z, Chen H, Yang R, Zheng W, Li S, Yang H, Wang J, Ehrlich SD, Nielsen R, Pedersen O, Kristiansen K, Wang J (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490:55–60
Fei N, Zhao L (2013) An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. ISME J 7:880–884
Vrieze A, Van Nood E, Holleman F, Salojarvi J, Kootte RS, Bartelsman JF, Dallinga-Thie GM, Ackermans MT, Serlie MJ, Oozeer R, Derrien M, Druesne A, Van Hylckama Vlieg JE, Bloks VW, Groen AK, Heilig HG, Zoetendal EG, Stroes ES, de Vos WM, Hoekstra JB, Nieuwdorp M (2012) Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 143(913–916):e917
Ubeda C, Lipuma L, Gobourne A, Viale A, Leiner I, Equinda M, Khanin R, Pamer EG (2012) Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice. J Exp Med 209:1445–1456
Kriegel M, Sefik E, Hill J, Wu H, Benoist C, Mathis D (2011) Naturally transmitted segmented filamentous bacteria segregate with diabetes protection in nonobese diabetic mice. Proc Natl Acad Sci U S A 108:11548–11553
Markle JG, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, von Bergen M, McCoy KD, Macpherson AJ, Danska JS (2013) Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science 339:1084–1088
Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sorensen SJ, Hansen LH, Jakobsen M (2010) Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 5:e9085
Membrez M, Blancher F, Jaquet M, Bibiloni R, Cani PD, Burcelin RG, Corthesy I, Mace K, Chou CJ (2008) Gut microbiota modulation with norfloxacin and ampicillin enhances glucose tolerance in mice. FASEB J 22:2416–2426
Karlsson FH, Tremaroli V, Nookaew I, Bergstrom G, Behre CJ, Fagerberg B, Nielsen J, Backhed F (2013) Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498:99–103
Chow J, Mazmanian SK (2010) A pathobiont of the microbiota balances host colonization and intestinal inflammation. Cell Host Microbe 7:265–276
Vaziri ND, Wong J, Pahl M, Piceno YM, Yuan J, DeSantis TZ, Ni Z, Nguyen TH, Andersen GL (2013) Chronic kidney disease alters intestinal microbial flora. Kidney Int 83:308–315
Schepers E, Glorieux G, Vanholder R (2010) The gut: the forgotten organ in uremia? Blood Purif 29:130–136
Kotanko P, Carter M, Levin NW (2006) Intestinal bacterial microflora–a potential source of chronic inflammation in patients with chronic kidney disease. Nephrol Dial Transplant 21:2057–2060
McIntyre CW, Harrison LE, Eldehni MT, Jefferies HJ, Szeto CC, John SG, Sigrist MK, Burton JO, Hothi D, Korsheed S, Owen PJ, Lai KB, Li PK (2011) Circulating endotoxemia: a novel factor in systemic inflammation and cardiovascular disease in chronic kidney disease. Clin J Am Soc Nephrol 6:133–141
Aronov PA, Luo FJ, Plummer NS, Quan Z, Holmes S, Hostetter TH, Meyer TW (2011) Colonic contribution to uremic solutes. J Am Soc Nephrol 22:1769–1776
Ranganathan N, Patel BG, Ranganathan P, Marczely J, Dheer R, Pechenyak B, Dunn SR, Verstraete W, Decroos K, Mehta R, Friedman EA (2006) In vitro and in vivo assessment of intraintestinal bacteriotherapy in chronic kidney disease. ASAIO J 52:70–79
Niwa T (2011) Role of indoxyl sulfate in the progression of chronic kidney disease and cardiovascular disease: experimental and clinical effects of oral sorbent AST-120. Ther Apher Dial 15:120–124
Borody T, Warren E, Leis S, Surace R, Ashman O, Siarakas S (2004) Bacteriotherapy using fecal flora toying with human motions. J Clin Gastroenterol 38:475–483
Gibson G, Roberfroid M (1995) Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 125:1401–1412
Holmes E, Kinross J, Gibson GR, Burcelin R, Jia W, Pettersson S, Nicholson JK (2012) Therapeutic modulation of microbiota-host metabolic interactions. Sci Transl Med 4, 137rv136
Smits L, Bouter K, de Vos W, Borody T, Nieuwdorp M (2013) Therapeutic Potential of Fecal Microbiota Transplantation. Gastroenterology 145:946–953
Borody T (2000) "Flora Power"– fecal bacteria cure chronic C. difficile diarrhea. Am J Gastroenterol 95:3028–3029
Khoruts A, Dicksved J, Jansson J, Sadowsky M (2010) Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol 44:354–360
Guarner F (2009) Prebiotics, probiotics and helminths: the 'natural' solution? Dig Dis 27:412–417
Fukuda S, Furuya H, Suzuki Y, Asanuma N, Hino T (2005) A new strain of Butyrivibrio fibrisolvens that has high ability to isomerize linoleic acid to conjugated linoleic acid. J Gen Appl Microbiol 51:105–113
West D, Delany J, Camet P, Blohm F, Truett A, Scimeca J (1998) Effects of conjugated linoleic acid on body fat and energy metabolism in the mouse. Am J Physiol 275(3 Pt 2):R667-72
Fukuda S, Suzuki Y, Murai M, Asanuma N, Hino T (2006) Isolation of a novel strain of Butyrivibrio fibrisolvens that isomerizes linoleic acid to conjugated linoleic acid without hydrogenation, and its utilization as a probiotic for animals. J Appl Microbiol 100:787–794
Ji YS, Kim HN, Park HJ, Lee JE, Yeo SY, Yang JS, Park SY, Yoon HS, Cho GS, Franz CM, Bomba A, Shin HK, Holzapfel WH (2012) Modulation of the murine microbiome with a concomitant anti-obesity effect by Lactobacillus rhamnosus GG and Lactobacillus sakei NR28. Benefic Microbes 3:13–22
Arora T, Anastasovska J, Gibson G, Tuohy K, Sharma RK, Bell J, Frost G (2012) Effect of Lactobacillus acidophilus NCDC 13 supplementation on the progression of obesity in diet-induced obese mice. Br J Nutr 108:1382–1389
Vendt N, Grünberg H, Tuure T, Malminiemi O, Wuolijoki E, Tillmann V, Sepp E, Korpela R (2006) Growth during the first 6 months of life in infants using formula enriched with Lactobacillus rhamnosus GG: double-blind, randomized trial. J Hum Nutr Diet 19:51–58
Luoto R, Kalliomaki M, Laitinen K, Isolauri E (2010) The impact of perinatal probiotic intervention on the development of overweight and obesity: follow-up study from birth to 10 years. Int J Obes (Lond) 34:1531–1537
Parnell JA, Reimer RA (2012) Prebiotic fibres dose-dependently increase satiety hormones and alter Bacteroidetes and Firmicutes in lean and obese JCR:LA-cp rats. Br J Nutr 107:601–613
Neyrinck AM, Possemiers S, Verstraete W, De Backer F, Cani PD, Delzenne NM (2012) Dietary modulation of clostridial cluster XIVa gut bacteria (Roseburia spp.) by chitin-glucan fiber improves host metabolic alterations induced by high-fat diet in mice. J Nutr Biochem 23:51–59
Neyrinck AM, Possemiers S, Druart C, Van de Wiele T, De Backer F, Cani PD, Larondelle Y, Delzenne NM (2011) Prebiotic effects of wheat arabinoxylan related to the increase in bifidobacteria, Roseburia and Bacteroides/Prevotella in diet-induced obese mice. PLoS One 6:e20944
Dewulf EM, Cani PD, Claus SP, Fuentes S, Puylaert PG, Neyrinck AM, Bindels LB, de Vos WM, Gibson GR, Thissen JP, Delzenne NM (2013) Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women. Gut 62:1112–1121
Davis LM, Martinez I, Walter J, Goin C, Hutkins RW (2011) Barcoded pyrosequencing reveals that consumption of galactooligosaccharides results in a highly specific bifidogenic response in humans. PLoS One 6:e25200
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This article is a contribution to the Special Issue on Microbiome, Immunity and Inflammation - Guest Editor: Hiroshi Ohno
Wanping Aw and Shinji Fukuda contributed equally to this work.
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Aw, W., Fukuda, S. Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach. Semin Immunopathol 37, 5–16 (2015). https://doi.org/10.1007/s00281-014-0456-2
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DOI: https://doi.org/10.1007/s00281-014-0456-2